pyTEMlib 0.2020.11.0__py3-none-any.whl → 0.2024.8.4__py3-none-any.whl

pyTEMlib/eels_dialog.py

@@ -1,486 +1,749 @@
-from PyQt5 import QtCore,  QtWidgets
-from pyTEMlib import eels_dlg
-
-import numpy as np
-
-from pyTEMlib import eels_tools as eels
-from pyTEMlib import interactive_eels
-import matplotlib.patches as patches
-from pyTEMlib import file_tools as ft
-import sidpy
-
-_version = 000
-
-
-class EELSDialog(QtWidgets.QDialog):
-    """
-    EELS Input Dialog for Chemical Analysis
-    """
-
-    def __init__(self, dataset=None):
-        super().__init__(None, QtCore.Qt.WindowStaysOnTopHint)
-        # Create an instance of the GUI
-        self.ui = eels_dlg.UiDialog(self)
-        # Run the .setup_ui() method to show the GUI
-        # self.ui.setup_ui(self)
-
-        self.set_action()
-
-        self.dataset = dataset
-        self.energy_scale = np.array([])
-        self.model = np.array([])
-        self.edges = {}
-        self.axis = None
-        self.show_regions = False
-        self.show()
-
-        if dataset is None:
-            # make a dummy dataset
-            dataset = ft.make_dummy_dataset(sidpy.DataTypes.SPECTRUM)
-
-        if not isinstance(dataset, sidpy.Dataset):
-            raise TypeError('dataset has to be a sidpy dataset')
-
-        self.set_dataset(dataset)
-        # TODO: set elements does not work correctly for periodic table
-        # selected_edges = eels.find_edges(dataset, sensitivity=3)
-        selected_edges = []
-        initial_elements = []
-
-        for edge in selected_edges:
-            initial_elements.append(edge.split('-')[0])
-        if len(initial_elements) > 0:
-            self.set_elements(initial_elements)
-
-        self.pt_dialog = interactive_eels.PeriodicTableDialog(energy_scale=self.energy_scale,
-                                                              initial_elements=initial_elements)
-        self.pt_dialog.signal_selected[list].connect(self.set_elements)
-
-        self.dataset.plot()
-
-        if hasattr(self.dataset.view, 'axes'):
-            self.axis = self.dataset.view.axes[-1]
-        elif hasattr(self.dataset.view, 'axis'):
-            self.axis = self.dataset.view.axis
-        self.figure = self.axis.figure
-
-        self.cid = self.figure.canvas.mpl_connect('draw_event', self.plot)
-
-        self.plot()
-        self.ui.edit4.setFocus()
-
-    def set_dataset(self, dataset):
-
-        self.dataset = dataset
-        if 'edges' not in self.dataset.metadata or self.dataset.metadata['edges'] == {}:
-            self.dataset.metadata['edges'] = {'0': {}, 'model': {}}
-        self.edges = self.dataset.metadata['edges']
-
-        spec_dim = -1
-        for dim, axis in dataset._axes.items():
-            if axis.dimension_type == sidpy.DimensionTypes.SPECTRAL:
-                spec_dim = dim
-        if spec_dim < 0:
-            raise TypeError('We need at least one SPECTRAL dimension')
-
-        self.spec_dim = spec_dim
-        self.energy_scale = dataset._axes[spec_dim].values
-
-        self.ui.edit2.setText(f"{self.energy_scale[-2]:.3f}")
-        if 'fit_area' not in self.edges:
-            self.edges['fit_area'] = {}
-        if 'fit_start' not in self.edges['fit_area']:
-            self.ui.edit1.setText(f"{self.energy_scale[50]:.3f}")
-            self.edges['fit_area']['fit_start'] = float(self.ui.edit1.displayText())
-        else:
-            self.ui.edit1.setText(f"{self.edges['fit_area']['fit_start']:.3f}")
-        if 'fit_end' not in self.edges['fit_area']:
-            self.ui.edit2.setText(f"{self.energy_scale[-2]:.3f}")
-            self.edges['fit_area']['fit_end'] = float(self.ui.edit2.displayText())
-        else:
-            self.ui.edit2.setText(f"{self.edges['fit_area']['fit_end']:.3f}")
-
-        self.update()
-
-    def update(self):
-        index = self.ui.list3.currentIndex()  # which edge
-        edge = self.edges[str(index)]
-
-        if 'Z' in edge:
-            self.ui.list5.setCurrentIndex(self.ui.edge_sym.index(edge['symmetry']))
-            self.ui.edit4.setText(str(edge['Z']))
-            self.ui.unit4.setText(edge['element'])
-            self.ui.edit6.setText(f"{edge['onset']:.2f}")
-            self.ui.edit7.setText(f"{edge['start_exclude']:.2f}")
-            self.ui.edit8.setText(f"{edge['end_exclude']:.2f}")
-            self.ui.edit9.setText(f"{edge['areal_density']:.2e}")
-        else:
-            self.ui.list3.setCurrentIndex(0)
-            self.ui.edit4.setText(str(0))
-            self.ui.unit4.setText(' ')
-            self.ui.edit6.setText(f"{0:.2f}")
-            self.ui.edit7.setText(f"{0:.2f}")
-            self.ui.edit8.setText(f"{0:.2f}")
-            self.ui.edit9.setText(f"{0:.2e}")
-
-    def update_element(self, z):
-        # We check whether this element is already in the
-        zz = eels.get_z(z)
-        for key, edge in self.edges.items():
-            if 'Z' in edge:
-                if zz == edge['Z']:
-                    return False
-
-        major_edge = ''
-        minor_edge = ''
-        all_edges = {}
-        x_section = eels.get_x_sections(zz)
-        edge_start = 10  # int(15./ft.get_slope(self.energy_scale)+0.5)
-        for key in x_section:
-            if len(key) == 2 and key[0] in ['K', 'L', 'M', 'N', 'O'] and key[1].isdigit():
-                if self.energy_scale[edge_start] < x_section[key]['onset'] < self.energy_scale[-edge_start]:
-                    if key in ['K1', 'L3', 'M5']:
-                        major_edge = key
-                    elif key in self.ui.edge_sym:
-                        if minor_edge == '':
-                            minor_edge = key
-                        if int(key[-1]) % 2 > 0:
-                            if int(minor_edge[-1]) % 2 == 0 or key[-1] > minor_edge[-1]:
-                                minor_edge = key
-
-                    all_edges[key] = {'onset': x_section[key]['onset']}
-
-        if major_edge != '':
-            key = major_edge
-        elif minor_edge != '':
-            key = minor_edge
-        else:
-            print(f'Could not find no edge of {zz} in spectrum')
-            return False
-
-        index = self.ui.list3.currentIndex()
-
-        if str(index) not in self.edges:
-            self.edges[str(index)] = {}
-
-        start_exclude = x_section[key]['onset'] - x_section[key]['excl before']
-        end_exclude = x_section[key]['onset'] + x_section[key]['excl after']
-
-        self.edges[str(index)] = {'Z': zz, 'symmetry': key, 'element': eels.elements[zz],
-                                  'onset': x_section[key]['onset'], 'end_exclude': end_exclude,
-                                  'start_exclude': start_exclude}
-        self.edges[str(index)]['all_edges'] = all_edges
-        self.edges[str(index)]['chemical_shift'] = 0.0
-        self.edges[str(index)]['areal_density'] = 0.0
-        self.edges[str(index)]['original_onset'] = self.edges[str(index)]['onset']
-        return True
-
-    def on_enter(self):
-        sender = self.sender()
-        edge_list = self.ui.list3
-
-        if sender.objectName() == 'fit_start_edit':
-            value = float(str(sender.displayText()).strip())
-            if value < self.energy_scale[0]:
-                value = self.energy_scale[0]
-            if value > self.energy_scale[-5]:
-                value = self.energy_scale[-5]
-            self.edges['fit_area']['fit_start'] = value
-            sender.setText(str(self.edges['fit_area']['fit_start']))
-        elif sender.objectName() == 'fit_end_edit':
-            value = float(str(sender.displayText()).strip())
-            if value < self.energy_scale[5]:
-                value = self.energy_scale[5]
-            if value > self.energy_scale[-1]:
-                value = self.energy_scale[-1]
-            self.edges['fit_area']['fit_end'] = value
-            sender.setText(str(self.edges['fit_area']['fit_end']))
-        elif sender.objectName() == 'element_edit':
-            if str(sender.displayText()).strip() == '0':
-                sender.setText('PT')
-                self.pt_dialog.energy_scale = self.energy_scale
-                self.pt_dialog.show()
-            else:
-                self.update_element(str(sender.displayText()).strip())
-            self.update()
-        elif sender.objectName() in ['onset_edit', 'excl_start_edit', 'excl_end_edit']:
-            self.check_area_consistency()
-
-        elif sender.objectName() == 'multiplier_edit':
-            index = edge_list.currentIndex()
-            self.edges[str(index)]['areal_density'] = float(self.ui.edit9.displayText())
-            if 'background' not in self.edges['model']:
-                print(' no background')
-                return
-            self.model = self.edges['model']['background']
-            for key in self.edges:
-                if key.isdigit():
-                    self.model = self.model + self.edges[key]['areal_density'] * self.edges[key]['data']
-            self.plot()
-        else:
-            return
-        if self.show_regions:
-            self.plot()
-
-    def sort_elements(self):
-        onsets = []
-        for index, edge in self.edges.items():
-            if index.isdigit():
-                onsets.append(float(edge['onset']))
-
-        arg_sorted = np.argsort(onsets)
-        edges = self.edges.copy()
-        for index, isorted in enumerate(arg_sorted):
-            self.edges[str(index)] = edges[str(isorted)].copy()
-
-        index = 0
-        edge = self.edges['0']
-        dispersion = self.energy_scale[1]-self.energy_scale[0]
-
-        while str(index + 1) in self.edges:
-            next_edge = self.edges[str(index + 1)]
-            if edge['end_exclude'] > next_edge['start_exclude'] - 5 * dispersion:
-                edge['end_exclude'] = next_edge['start_exclude'] - 5 * dispersion
-            edge = next_edge
-            index += 1
-
-        if edge['end_exclude'] > self.energy_scale[-3]:
-            edge['end_exclude'] = self.energy_scale[-3]
-
-    def set_elements(self, selected_elements):
-
-        edge_list = self.ui.list3
-        index = edge_list.currentIndex()
-
-        for elem in selected_elements:
-            if self.update_element(elem):
-                index = edge_list.currentIndex()
-                edge_list.setCurrentIndex(index + 1)
-        self.sort_elements()
-        edge_list.setCurrentIndex(index)
-        self.update()
-
-    def plot(self):
-        self.energy_scale = self.dataset._axes[self.spec_dim].values
-        if self.dataset.data_type == sidpy.DataTypes.SPECTRAL_IMAGE:
-            spectrum = self.dataset.view.get_spectrum()
-            self.axis = self.dataset.view.axes[1]
-        else:
-            spectrum = np.array(self.dataset)
-            self.axis = self.dataset.view.axis
-
-        if self.ui.select10.isChecked():
-            if 'experiment' in self.dataset.metadata:
-                exp = self.dataset.metadata['experiment']
-                if 'convergence_angle' not in exp:
-                    raise ValueError('need a convergence_angle in experiment of metadata dictionary ')
-                alpha = exp['convergence_angle']
-                beta = exp['collection_angle']
-                beam_kv = exp['acceleration_voltage']
-
-                eff_beta = eels.effective_collection_angle(self.energy_scale, alpha, beta, beam_kv)
-                edges = eels.make_cross_sections(self.edges, np.array(self.energy_scale), beam_kv, eff_beta)
-                self.edges = eels.fit_edges2(spectrum, self.energy_scale, edges)
-                areal_density = []
-                elements = []
-                for key in edges:
-                    if key.isdigit():  # only edges have numbers in that dictionary
-                        elements.append(edges[key]['element'])
-                        areal_density.append(edges[key]['areal_density'])
-                areal_density = np.array(areal_density)
-                out_string = '\nRelative composition: \n'
-                for i, element in enumerate(elements):
-                    out_string += f'{element}: {areal_density[i] / areal_density.sum() * 100:.1f}%  '
-
-                self.model = self.edges['model']['spectrum']
-                self.update()
-
-        x_limit = self.axis.get_xlim()
-        y_limit = self.axis.get_ylim()
-        self.axis.clear()
-
-        self.axis.plot(self.energy_scale, spectrum, label='spectrum')
-        if len(self.model) > 1:
-            self.axis.plot(self.energy_scale, self.model, label='model')
-            self.axis.plot(self.energy_scale, spectrum - self.model, label='difference')
-            self.axis.plot(self.energy_scale, (spectrum - self.model) / np.sqrt(spectrum), label='Poisson')
-            self.axis.legend()
-        self.axis.set_xlim(x_limit)
-        self.axis.set_ylim(y_limit)
-
-        if self.ui.show_edges.isChecked():
-            self.show_edges()
-        if self.show_regions:
-            self.plot_regions()
-        self.figure.canvas.draw_idle()
-
-    def plot_regions(self):
-        y_min, y_max = self.axis.get_ylim()
-        height = y_max - y_min
-
-        rect = []
-        if 'fit_area' in self.edges:
-            color = 'blue'
-            alpha = 0.2
-            x_min = self.edges['fit_area']['fit_start']
-            width = self.edges['fit_area']['fit_end'] - x_min
-            rect.append(patches.Rectangle((x_min, y_min), width, height,
-                                          edgecolor=color, alpha=alpha, facecolor=color))
-            self.axis.add_patch(rect[0])
-            self.axis.text(x_min, y_max, 'fit region', verticalalignment='top')
-        color = 'red'
-        alpha = 0.5
-        for key in self.edges:
-            if key.isdigit():
-                x_min = self.edges[key]['start_exclude']
-                width = self.edges[key]['end_exclude']-x_min
-                rect.append(patches.Rectangle((x_min, y_min), width, height,
-                                              edgecolor=color, alpha=alpha, facecolor=color))
-                self.axis.add_patch(rect[-1])
-                self.axis.text(x_min, y_max, f"exclude\n edge {int(key)+1}", verticalalignment='top')
-
-    def show_edges(self):
-        x_min, x_max = self.axis.get_xlim()
-        y_min, y_max = self.axis.get_ylim()
-
-        for key, edge in self.edges.items():
-            i = 0
-            if key.isdigit():
-                element = edge['element']
-                for sym in edge['all_edges']:
-                    x = edge['all_edges'][sym]['onset'] + edge['chemical_shift']
-                    if x_min < x < x_max:
-                        self.axis.text(x, y_max, '\n' * i + f"{element}-{sym}",
-                                       verticalalignment='top', color='black')
-                        self.axis.axvline(x, ymin=0, ymax=1, color='gray')
-                        i += 1
-
-    def check_area_consistency(self):
-        if self.dataset is None:
-            return
-        onset = float(self.ui.edit6.displayText())
-        excl_start = float(self.ui.edit7.displayText())
-        excl_end = float(self.ui.edit8.displayText())
-        if onset < self.energy_scale[2]:
-            onset = self.energy_scale[2]
-            excl_start = self.energy_scale[2]
-        if onset > self.energy_scale[-2]:
-            onset = self.energy_scale[-2]
-            excl_end = self.energy_scale[-2]
-        if excl_start > onset:
-            excl_start = onset
-        if excl_end < onset:
-            excl_end = onset
-
-        index = self.ui.list3.currentIndex()
-        self.edges[str(index)]['chemical_shift'] = onset - self.edges[str(index)]['original_onset']
-        self.edges[str(index)]['onset'] = onset
-        self.edges[str(index)]['end_exclude'] = excl_end
-        self.edges[str(index)]['start_exclude'] = excl_start
-
-        self.update()
-
-    def on_list_enter(self):
-        sender = self.sender()
-
-        if sender.objectName() == 'edge_list':
-            index = self.ui.list3.currentIndex()
-
-            number_of_edges = 0
-            for key in self.edges:
-                if key.isdigit():
-                    if int(key) > number_of_edges:
-                        number_of_edges = int(key)
-            number_of_edges += 1
-            if index > number_of_edges:
-                index = number_of_edges
-            self.ui.list3.setCurrentIndex(index)
-            if str(index) not in self.edges:
-                self.edges[str(index)] = {'Z': 0, 'symmetry': 'K1', 'element': 'H', 'onset': 0, 'end_exclude': 0,
-                                          'start_exclude': 0, 'areal_density': 0}
-
-            self.update()
-        elif sender.objectName() == 'symmetry_list':
-            sym = self.ui.list5.currentText()
-            index = self.ui.list3.currentIndex()
-            zz = self.edges[str(index)]['Z']
-            if zz > 1:
-                x_section = eels.get_x_sections(zz)
-                if sym in x_section:
-                    start_exclude = x_section[sym]['onset'] - x_section[sym]['excl before']
-                    end_exclude = x_section[sym]['onset'] + x_section[sym]['excl after']
-                    self.edges[str(index)].update({'symmetry': sym, 'onset': x_section[sym]['onset'],
-                                                   'end_exclude': end_exclude, 'start_exclude': start_exclude})
-                    self.edges[str(index)]['chemical_shift'] = 0.0
-                    self.edges[str(index)]['areal_density'] = 0.0
-                    self.edges[str(index)]['original_onset'] = self.edges[index]['onset']
-                    self.update()
-        elif sender.objectName() == 'symmetry_method':
-            self.ui.select5.setCurrentIndex(0)
-
-    def on_check(self):
-        sender = self.sender()
-
-        if sender.objectName() == 'edge_check':
-            self.show_regions = sender.isChecked()
-        self.plot()
-
-    def do_all_button_click(self):
-        pass
-
-    def do_fit_button_click(self):
-        if 'experiment' in self.dataset.metadata:
-            exp = self.dataset.metadata['experiment']
-            if 'convergence_angle' not in exp:
-                raise ValueError('need a convergence_angle in experiment of metadata dictionary ')
-            alpha = exp['convergence_angle']
-            beta = exp['collection_angle']
-            beam_kv = exp['acceleration_voltage']
-
-        else:
-            raise ValueError('need a experiment parameter in metadata dictionary')
-        self.energy_scale = self.dataset._axes[self.spec_dim].values
-        eff_beta = eels.effective_collection_angle(self.energy_scale, alpha, beta, beam_kv)
-
-        edges = eels.make_cross_sections(self.edges, np.array(self.energy_scale), beam_kv, eff_beta)
-
-        if self.dataset.data_type == sidpy.DataTypes.SPECTRAL_IMAGE:
-            spectrum = self.dataset.view.get_spectrum()
-        else:
-            spectrum = self.dataset
-        self.edges = eels.fit_edges2(spectrum, self.energy_scale, edges)
-        areal_density = []
-        elements = []
-        for key in edges:
-            if key.isdigit():  # only edges have numbers in that dictionary
-                elements.append(edges[key]['element'])
-                areal_density.append(edges[key]['areal_density'])
-        areal_density = np.array(areal_density)
-        out_string = '\nRelative composition: \n'
-        for i, element in enumerate(elements):
-            out_string += f'{element}: {areal_density[i] / areal_density.sum() * 100:.1f}%  '
-
-        self.model = self.edges['model']['spectrum']
-        self.update()
-        self.plot()
-
-    def set_action(self):
-        self.ui.edit1.editingFinished.connect(self.on_enter)
-        self.ui.edit2.editingFinished.connect(self.on_enter)
-        self.ui.list3.activated[str].connect(self.on_list_enter)
-        self.ui.check3.clicked.connect(self.on_check)
-        self.ui.edit4.editingFinished.connect(self.on_enter)
-        self.ui.list5.activated[str].connect(self.on_list_enter)
-        self.ui.select5.activated[str].connect(self.on_list_enter)
-
-        self.ui.edit6.editingFinished.connect(self.on_enter)
-        self.ui.edit7.editingFinished.connect(self.on_enter)
-        self.ui.edit8.editingFinished.connect(self.on_enter)
-        self.ui.edit9.editingFinished.connect(self.on_enter)
-
-        self.ui.check10.clicked.connect(self.on_check)
-        self.ui.select10.clicked.connect(self.on_check)
-        self.ui.show_edges.clicked.connect(self.on_check)
-
-        self.ui.do_all_button.clicked.connect(self.do_all_button_click)
-        self.ui.do_fit_button.clicked.connect(self.do_fit_button_click)
+"""
+Author: Gerd Duscher
+"""
+
+
+import numpy as np
+import warnings
+
+import ipywidgets
+import IPython.display
+# from IPython.display import display
+import matplotlib
+import matplotlib.pylab as plt
+import matplotlib.patches as patches
+
+from pyTEMlib import file_tools as ft
+from pyTEMlib import eels_tools as eels
+from pyTEMlib import eels_dialog_utilities
+
+import sidpy
+
+
+class CurveVisualizer(object):
+    """Plots a sidpy.Dataset with spectral dimension-type
+
+    """
+    def __init__(self, dset, spectrum_number=None, axis=None, leg=None, **kwargs):
+        if not isinstance(dset, sidpy.Dataset):
+            raise TypeError('dset should be a sidpy.Dataset object')
+        if axis is None:
+            self.fig = plt.figure()
+            self.axis = self.fig.add_subplot(1, 1, 1)
+        else:
+            self.axis = axis
+            self.fig = axis.figure
+
+        self.dset = dset
+        self.selection = []
+        [self.spec_dim, self.energy_scale] = ft.get_dimensions_by_type('spectral', self.dset)[0]
+
+        self.lined = dict()
+        self.plot(**kwargs)
+
+    def plot(self, **kwargs):
+        if self.dset.data_type.name == 'IMAGE_STACK':
+            line1, = self.axis.plot(self.energy_scale.values, self.dset[0, 0], label='spectrum', **kwargs)
+        else:
+            line1, = self.axis.plot(self.energy_scale.values, self.dset, label='spectrum', **kwargs)
+        lines = [line1]
+        if 'add2plot' in self.dset.metadata:
+            data = self.dset.metadata['add2plot']
+            for key, line in data.items():
+                line_add, = self.axis.plot(self.energy_scale.values,  line['data'], label=line['legend'])
+                lines.append(line_add)
+
+            legend = self.axis.legend(loc='upper right', fancybox=True, shadow=True)
+            legend.get_frame().set_alpha(0.4)
+
+            for legline, origline in zip(legend.get_lines(), lines):
+                legline.set_picker(True)
+                legline.set_pickradius(5)  # 5 pts tolerance
+                self.lined[legline] = origline
+            self.fig.canvas.mpl_connect('pick_event', self.onpick)
+
+        self.axis.axhline(0, color='gray', alpha=0.6)
+        self.axis.set_xlabel(self.dset.labels[0])
+        self.axis.set_ylabel(self.dset.data_descriptor)
+        self.axis.ticklabel_format(style='sci', scilimits=(-2, 3))
+        self.fig.canvas.draw_idle()
+
+    def update(self, **kwargs):
+        x_limit = self.axis.get_xlim()
+        y_limit = self.axis.get_ylim()
+        self.axis.clear()
+        self.plot(**kwargs)
+        self.axis.set_xlim(x_limit)
+        self.axis.set_ylim(y_limit)
+
+    def onpick(self, event):
+        # on the pick event, find the orig line corresponding to the
+        # legend proxy line, and toggle the visibility
+        legline = event.artist
+        origline = self.lined[legline]
+        vis = not origline.get_visible()
+        origline.set_visible(vis)
+        # Change the alpha on the line in the legend, so we can see what lines
+        # have been toggled
+        if vis:
+            legline.set_alpha(1.0)
+        else:
+            legline.set_alpha(0.2)
+        self.fig.canvas.draw()
+
+def get_core_loss_sidebar():
+    side_bar = ipywidgets.GridspecLayout(14, 3,width='auto', grid_gap="0px")
+
+    
+    row = 0
+    side_bar[row, :3] = ipywidgets.ToggleButton(description='Fit Area',
+                     layout=ipywidgets.Layout(width='auto', grid_area='header'),
+                     tooltip='Shows fit regions and regions excluded from fit', 
+                     button_style='info') #ipywidgets.ButtonStyle(button_color='lightblue'))
+    row += 1
+    side_bar[row, :2] = ipywidgets.FloatText(value=7.5,description='Fit Start:', disabled=False, color='black', layout=ipywidgets.Layout(width='200px'))
+    side_bar[row, 2] = ipywidgets.widgets.Label(value="eV", layout=ipywidgets.Layout(width='20px'))
+    row += 1
+    side_bar[row, :2] = ipywidgets.FloatText(value=0.1, description='Fit End:', disabled=False, color='black', layout=ipywidgets.Layout(width='200px'))
+    side_bar[row, 2] = ipywidgets.widgets.Label(value="eV", layout=ipywidgets.Layout(width='20px'))
+    
+    row += 1
+    
+    side_bar[row, :3] = ipywidgets.Button(description='Elements',
+                     layout=ipywidgets.Layout(width='auto', grid_area='header'),
+                     style=ipywidgets.ButtonStyle(button_color='lightblue'))
+    row += 1
+    side_bar[row, :2] = ipywidgets.Dropdown(
+            options=[('Edge 1', 0), ('Edge 2', 1), ('Edge 3', 2), ('Edge 4', 3),('Add Edge', -1)],
+            value=0,
+            description='Edges:',
+            disabled=False,
+            layout=ipywidgets.Layout(width='200px'))
+    """side_bar[row,2] = ipywidgets.ToggleButton(
+            description='Regions',
+            disabled=False,
+            button_style='', # 'success', 'info', 'warning', 'danger' or ''
+            tooltip='Shows fit regions and regions excluded from fit', 
+            layout=ipywidgets.Layout(width='100px')
+        )
+    """
+    row += 1
+    side_bar[row, :2] = ipywidgets.IntText(value=7.5,description='Z:', disabled=False, color='black', layout=ipywidgets.Layout(width='200px'))
+    side_bar[row, 2] = ipywidgets.widgets.Label(value="", layout=ipywidgets.Layout(width='100px'))
+    row += 1
+    side_bar[row, :2] = ipywidgets.Dropdown(
+            options=['K1','L3', 'M5', 'M3', 'M1', 'N7', 'N5', 'N3', 'N1'],
+            value='K1',
+            description='Symmetry:',
+            disabled=False,
+            layout=ipywidgets.Layout(width='200px'))
+    row += 1
+    side_bar[row, :2] = ipywidgets.FloatText(value=0.1, description='Onset:', disabled=False, color='black', layout=ipywidgets.Layout(width='200px'))
+    side_bar[row, 2] = ipywidgets.widgets.Label(value="eV", layout=ipywidgets.Layout(width='100px'))
+    row += 1
+    side_bar[row, :2] = ipywidgets.FloatText(value=0.1, description='Excl.Start:', disabled=False, color='black', layout=ipywidgets.Layout(width='200px'))
+    side_bar[row, 2] = ipywidgets.widgets.Label(value="eV", layout=ipywidgets.Layout(width='100px'))
+    row += 1
+    side_bar[row, :2] = ipywidgets.FloatText(value=0.1, description='Excl.End:', disabled=False, color='black', layout=ipywidgets.Layout(width='200px'))
+    side_bar[row, 2] = ipywidgets.widgets.Label(value="eV", layout=ipywidgets.Layout(width='100px'))
+    row += 1
+    side_bar[row, :2] = ipywidgets.FloatText(value=0.1, description='Mutliplier:', disabled=False, color='black', layout=ipywidgets.Layout(width='200px'))
+    side_bar[row, 2] = ipywidgets.widgets.Label(value="a.u.", layout=ipywidgets.Layout(width='100px'))
+    row += 1
+    
+    side_bar[row, :3] = ipywidgets.Button(description='Quantification',
+                     layout=ipywidgets.Layout(width='auto', grid_area='header'),
+                     style=ipywidgets.ButtonStyle(button_color='lightblue'))
+    
+    row += 1
+    side_bar[row,0] = ipywidgets.ToggleButton(
+            description='Probabiity',
+            disabled=False,
+            button_style='', # 'success', 'info', 'warning', 'danger' or ''
+            tooltip='Changes y-axis to probability of flux is given', 
+            layout=ipywidgets.Layout(width='100px')
+        )
+    side_bar[row,1] = ipywidgets.ToggleButton(
+            description='Conv.LL',
+            disabled=False,
+            button_style='', # 'success', 'info', 'warning', 'danger' or ''
+            tooltip='Changes y-axis to probability of flux is given', 
+            layout=ipywidgets.Layout(width='100px')
+        )
+    side_bar[row,2] = ipywidgets.ToggleButton(
+            description='Show Edges',
+            disabled=False,
+            button_style='', # 'success', 'info', 'warning', 'danger' or ''
+            tooltip='Changes y-axis to probability of flux is given', 
+            layout=ipywidgets.Layout(width='100px')
+        )
+    
+    row += 1
+    side_bar[row,0] = ipywidgets.ToggleButton(
+            description='Do All',
+            disabled=False,
+            button_style='', # 'success', 'info', 'warning', 'danger' or ''
+            tooltip='Fits all spectra of spectrum image', 
+            layout=ipywidgets.Layout(width='100px')
+            )
+
+    side_bar[row,1] = ipywidgets.IntProgress(value=0, min=0, max=10, description=' ', bar_style='', # 'success', 'info', 'warning', 'danger' or ''
+                                             style={'bar_color': 'maroon'}, orientation='horizontal')
+    return side_bar
+
+
+
+class CompositionWidget(object):
+    def __init__(self, datasets=None, key=None):
+        
+        if not isinstance(datasets, dict):
+            raise TypeError('dataset or first item has to be a sidpy dataset')
+        self.datasets = datasets
+
+        
+        self.model = []
+        self.sidebar = get_core_loss_sidebar()
+        
+        self.set_dataset(key)
+        
+        self.periodic_table = eels_dialog_utilities.PeriodicTableWidget(self.energy_scale)
+        self.elements_cancel_button = ipywidgets.Button(description='Cancel')
+        self.elements_select_button = ipywidgets.Button(description='Select')
+        self.elements_auto_button = ipywidgets.Button(description='Auto ID')
+       
+        self.periodic_table_panel = ipywidgets.VBox([self.periodic_table.periodic_table,
+                                                     ipywidgets.HBox([self.elements_cancel_button, self.elements_auto_button, self.elements_select_button])])
+        
+                                      
+        self.app_layout = ipywidgets.AppLayout(
+            left_sidebar=self.sidebar,
+            center=self.view.panel,
+            footer=None,#message_bar,
+            pane_heights=[0, 10, 0],
+            pane_widths=[4, 10, 0],
+        )
+        self.set_action()
+        IPython.display.display(self.app_layout)
+
+        
+    def line_select_callback(self, x_min, x_max):
+            self.start_cursor.value = np.round(x_min,3)
+            self.end_cursor.value = np.round(x_max, 3)
+
+            self.start_channel = np.searchsorted(self.datasets[self.key].energy_loss, self.start_cursor.value)
+            self.end_channel = np.searchsorted(self.datasets[self.key].energy_loss, self.end_cursor.value)
+       
+            
+    def plot(self, scale=True):
+        self.view.change_y_scale = self.change_y_scale
+        self.view.y_scale = self.y_scale
+        self.energy_scale = self.dataset.energy_loss.values
+        
+        if self.dataset.data_type == sidpy.DataType.SPECTRAL_IMAGE:
+            spectrum = self.view.get_spectrum()
+        else:
+            spectrum = self.dataset
+        if len(self.model) > 1:
+            additional_spectra = {'model': self.model,
+                                  'difference': spectrum-self.model}   
+        else:
+            additional_spectra = None
+        self.view.plot(scale=True, additional_spectra=additional_spectra )
+        self.change_y_scale = 1.
+    
+        if self.sidebar[12, 2].value:
+            self.show_edges()
+        if self.sidebar[0, 0].value:
+            self.plot_regions()
+        self.view.figure.canvas.draw_idle()
+        
+        
+    def plot_regions(self):
+        axis = self.view.figure.gca()
+        y_min, y_max = axis.get_ylim()
+        height = y_max - y_min
+
+        rect = []
+        if 'fit_area' in self.edges:
+            color = 'blue'
+            alpha = 0.2
+            x_min = self.edges['fit_area']['fit_start']
+            width = self.edges['fit_area']['fit_end'] - x_min
+            rect.append(patches.Rectangle((x_min, y_min), width, height,
+                                          edgecolor=color, alpha=alpha, facecolor=color))
+            axis.add_patch(rect[0])
+            axis.text(x_min, y_max, 'fit region', verticalalignment='top')
+        color = 'red'
+        alpha = 0.5
+        
+        for key in self.edges:
+            if key.isdigit():
+                x_min = self.edges[key]['start_exclude']
+                width = self.edges[key]['end_exclude']-x_min
+                rect.append(patches.Rectangle((x_min, y_min), width, height,
+                                              edgecolor=color, alpha=alpha, facecolor=color))
+                axis.add_patch(rect[-1])
+                axis.text(x_min, y_max, f"exclude\n edge {int(key)+1}", verticalalignment='top')
+
+    def show_edges(self):
+        axis = self.view.figure.gca()
+        x_min, x_max = axis.get_xlim()
+        y_min, y_max = axis.get_ylim()
+        
+        for key, edge in self.edges.items():
+            i = 0
+            if key.isdigit():
+                element = edge['element']
+                for sym in edge['all_edges']:
+                    x = edge['all_edges'][sym]['onset'] + edge['chemical_shift']
+                    if x_min < x < x_max:
+                        axis.text(x, y_max, '\n' * i + f"{element}-{sym}",
+                                       verticalalignment='top', color='black')
+                        axis.axvline(x, ymin=0, ymax=1, color='gray')
+                        i += 1
+
+        
+    
+        
+    def set_dataset(self, set_key):
+        spectrum_list = []
+        self.spectrum_keys_list = []
+        reference_list =[('None', -1)]
+        
+        for index, key in enumerate(self.datasets.keys()):
+            if '_rel' not in key:
+                if 'Reference' not in key :
+                    if 'SPECTR' in self.datasets[key].data_type.name:
+                        spectrum_list.append((f'{key}: {self.datasets[key].title}', index)) 
+                        self.spectrum_keys_list.append(key)
+                reference_list.append((f'{key}: {self.datasets[key].title}', index))  
+        
+        if set_key in self.spectrum_keys_list:
+            self.key = set_key
+        else:
+            self.key = self.spectrum_keys_list[-1]
+        self.dataset = self.datasets[self.key]
+        
+        self.spec_dim = self.dataset.get_spectral_dims(return_axis=True)[0]
+
+        self.energy_scale = self.spec_dim.values
+        self.dd = (self.energy_scale[0], self.energy_scale[1])
+
+        self.dataset.metadata['experiment']['offset'] = self.energy_scale[0]
+        self.dataset.metadata['experiment']['dispersion'] = self.energy_scale[1] - self.energy_scale[0]
+        if 'edges' not in self.dataset.metadata or self.dataset.metadata['edges'] == {}:
+            self.dataset.metadata['edges'] = {'0': {}, 'model': {}, 'use_low_loss': False}
+       
+        self.edges = self.dataset.metadata['edges']
+        if '0' not in self.edges:
+            self.edges['0'] = {}
+        
+        if 'fit_area' not in self.edges:
+            self.edges['fit_area'] = {}
+        if 'fit_start' not in self.edges['fit_area']:
+            self.sidebar[1,0].value = np.round(self.energy_scale[50], 3)
+            self.edges['fit_area']['fit_start'] = self.sidebar[1,0].value 
+        else:
+            self.sidebar[1,0].value = np.round(self.edges['fit_area']['fit_start'],3)
+        if 'fit_end' not in self.edges['fit_area']:
+            self.sidebar[2,0].value = np.round(self.energy_scale[-2], 3)
+            self.edges['fit_area']['fit_end'] = self.sidebar[2,0].value 
+        else:
+            self.sidebar[2,0].value = np.round(self.edges['fit_area']['fit_end'],3)
+        
+        if self.dataset.data_type.name == 'SPECTRAL_IMAGE':
+            if 'SI_bin_x' not in self.dataset.metadata['experiment']:
+                self.dataset.metadata['experiment']['SI_bin_x'] = 1
+                self.dataset.metadata['experiment']['SI_bin_y'] = 1
+
+            bin_x = self.dataset.metadata['experiment']['SI_bin_x']
+            bin_y = self.dataset.metadata['experiment']['SI_bin_y']
+            # self.dataset.view.set_bin([bin_x, bin_y])
+        if self.dataset.data_type.name =='SPECTRAL_IMAGE':
+            self.view = eels_dialog_utilities.SIPlot(self.dataset)
+        else:
+            self.view = eels_dialog_utilities.SpectrumPlot(self.dataset)    
+        self.y_scale = 1.0
+        self.change_y_scale = 1.0
+        
+        self.update()
+        
+    def update_element(self, z=0, index=-1):
+        # We check whether this element is already in the
+        if z == 0:
+            z = self.sidebar[5,0].value
+    
+        zz = eels.get_z(z)
+        for key, edge in self.edges.items():
+            if key.isdigit():
+                if 'z' in edge:
+                    if zz == edge['z']:
+                        return False
+
+        major_edge = ''
+        minor_edge = ''
+        all_edges = {}
+        x_section = eels.get_x_sections(zz)
+        edge_start = 10  # int(15./ft.get_slope(self.energy_scale)+0.5)
+        for key in x_section:
+            if len(key) == 2 and key[0] in ['K', 'L', 'M', 'N', 'O'] and key[1].isdigit():
+                if self.energy_scale[edge_start] < x_section[key]['onset'] < self.energy_scale[-edge_start]:
+                    if key in ['K1', 'L3', 'M5']:
+                        major_edge = key
+                    elif key in self.sidebar[6,0].options:
+                        if minor_edge == '':
+                            minor_edge = key
+                        if int(key[-1]) % 2 > 0:
+                            if int(minor_edge[-1]) % 2 == 0 or key[-1] > minor_edge[-1]:
+                                minor_edge = key
+
+                    all_edges[key] = {'onset': x_section[key]['onset']}
+
+        if major_edge != '':
+            key = major_edge
+        elif minor_edge != '':
+            key = minor_edge
+        else:
+            print(f'Could not find no edge of {zz} in spectrum')
+            return False
+        if index == -1:
+            index = self.sidebar[4, 0].value
+        # self.ui.dialog.setWindowTitle(f'{index}, {zz}')
+
+        if str(index) not in self.edges:
+            self.edges[str(index)] = {}
+
+        start_exclude = x_section[key]['onset'] - x_section[key]['excl before']
+        end_exclude = x_section[key]['onset'] + x_section[key]['excl after']
+
+        self.edges[str(index)] = {'z': zz, 'symmetry': key, 'element': eels.elements[zz],
+                                  'onset': x_section[key]['onset'], 'end_exclude': end_exclude,
+                                  'start_exclude': start_exclude}
+        self.edges[str(index)]['all_edges'] = all_edges
+        self.edges[str(index)]['chemical_shift'] = 0.0
+        self.edges[str(index)]['areal_density'] = 0.0
+        self.edges[str(index)]['original_onset'] = self.edges[str(index)]['onset']
+        return True
+    
+    def sort_elements(self):
+        onsets = []
+        for index, edge in self.edges.items():
+            if index.isdigit():
+                onsets.append(float(edge['onset']))
+
+        arg_sorted = np.argsort(onsets)
+        edges = self.edges.copy()
+        for index, i_sorted in enumerate(arg_sorted):
+            self.edges[str(index)] = edges[str(i_sorted)].copy()
+
+        index = 0
+        edge = self.edges['0']
+        dispersion = self.energy_scale[1]-self.energy_scale[0]
+
+        while str(index + 1) in self.edges:
+            next_edge = self.edges[str(index + 1)]
+            if edge['end_exclude'] > next_edge['start_exclude'] - 5 * dispersion:
+                edge['end_exclude'] = next_edge['start_exclude'] - 5 * dispersion
+            edge = next_edge
+            index += 1
+
+        if edge['end_exclude'] > self.energy_scale[-3]:
+            edge['end_exclude'] = self.energy_scale[-3]
+
+    def set_elements(self, value=0):
+        selected_elements = self.periodic_table.get_output()
+        edges = self.edges.copy()
+        to_delete = []
+        old_elements = []
+        if len(selected_elements) > 0:
+            for key in self.edges:
+                if key.isdigit():
+                    to_delete.append(key)
+                    old_elements.append(self.edges[key]['element'])
+
+        for key in to_delete:
+            edges[key] = self.edges[key]
+            del self.edges[key]
+    
+        for index, elem in enumerate(selected_elements):
+            if elem  in old_elements:
+                self.edges[str(index)] = edges[str(old_elements.index(elem))]   
+            else:
+                self.update_element(elem, index=index)
+        self.sort_elements()
+        self.update()
+        self.set_figure_pane()
+
+    def set_element(self, elem):
+        self.update_element(self.sidebar[5, 0].value)
+        # self.sort_elements()
+        self.update()
+       
+    def cursor2energy_scale(self, value):
+        dispersion = (self.end_cursor.value - self.start_cursor.value) / (self.end_channel - self.start_channel)
+        self.datasets[self.key].energy_loss *= (self.sidebar[3, 0].value/dispersion)
+        self.sidebar[3, 0].value = dispersion
+        offset = self.start_cursor.value - self.start_channel * dispersion
+        self.datasets[self.key].energy_loss += (self.sidebar[2, 0].value-self.datasets[self.key].energy_loss[0])
+        self.sidebar[2, 0].value = offset
+        self.plot()
+        
+    def set_fit_area(self, value):
+        if self.sidebar[1,0].value > self.sidebar[2,0].value:
+            self.sidebar[1,0].value = self.sidebar[2,0].value -1
+        if self.sidebar[1,0].value < self.energy_scale[0]:
+            self.sidebar[1,0].value = self.energy_scale[0]
+        if self.sidebar[2,0].value > self.energy_scale[-1]:
+            self.sidebar[2,0].value = self.energy_scale[-1]
+        self.edges['fit_area']['fit_start'] = self.sidebar[1,0].value 
+        self.edges['fit_area']['fit_end'] = self.sidebar[2,0].value 
+        
+        self.plot()
+        
+    def set_y_scale(self, value):  
+        self.change_y_scale = 1/self.y_scale
+        self.y_scale = 1.0
+        if self.dataset.metadata['experiment']['flux_ppm'] > 0:
+            if self.sidebar[12, 0].value:
+                dispersion = self.energy_scale[1] - self.energy_scale[0]
+                self.y_scale = 1/self.dataset.metadata['experiment']['flux_ppm'] * dispersion
+            
+        self.change_y_scale *= self.y_scale
+        self.update()
+        self.plot()
+
+    def auto_id(self, value=0):
+        found_edges = eels.auto_id_edges(self.dataset)
+        if len(found_edges) > 0:
+            self.periodic_table.elements_selected = found_edges
+            self.periodic_table.update()
+        
+    def find_elements(self, value=0):
+        
+        if '0' not in self.edges:
+            self.edges['0'] = {}
+        # found_edges = eels.auto_id_edges(self.dataset)
+        found_edges = {}
+
+        selected_elements = []
+        elements = self.edges.copy()
+
+        for key in self.edges:
+            if key.isdigit():
+                if 'element' in self.edges[key]:
+                    selected_elements.append(self.edges[key]['element'])
+        self.periodic_table.elements_selected = selected_elements
+        self.periodic_table.update()
+        self.app_layout.center = self.periodic_table_panel # self.periodic_table.periodic_table
+
+    def set_figure_pane(self, value=0):
+        
+        self.app_layout.center = self.view.panel
+    
+    def update(self, index=0):
+        
+        index = self.sidebar[4,0].value  # which edge
+        if index < 0:
+            options  = list(self.sidebar[4,0].options)
+            options.insert(-1, (f'Edge {len(self.sidebar[4,0].options)}', len(self.sidebar[4,0].options)-1))
+            self.sidebar[4,0].options= options
+            self.sidebar[4,0].value = len(self.sidebar[4,0].options)-2
+        if str(index) not in self.edges:
+            self.edges[str(index)] = {'z': 0,  'element': 'x', 'symmetry': 'K1', 'onset': 0, 'start_exclude': 0, 'end_exclude':0,
+                                     'areal_density': 0, 'chemical_shift':0}
+        if 'z' not in self.edges[str(index)]:
+             self.edges[str(index)] = {'z': 0,  'element': 'x', 'symmetry': 'K1', 'onset': 0, 'start_exclude': 0, 'end_exclude':0,
+                                      'areal_density': 0, 'chemical_shift':0}
+        edge = self.edges[str(index)]
+            
+        self.sidebar[5,0].value = edge['z']
+        self.sidebar[5,2].value = edge['element']
+        self.sidebar[6,0].value = edge['symmetry']
+        self.sidebar[7,0].value = edge['onset']
+        self.sidebar[8,0].value = edge['start_exclude']
+        self.sidebar[9,0].value = edge['end_exclude']
+        if self.y_scale == 1.0:
+            self.sidebar[10, 0].value = edge['areal_density']
+            self.sidebar[10, 2].value =  'a.u.'
+        else:
+            dispersion = self.energy_scale[1]-self.energy_scale[0]
+            self.sidebar[10, 0].value = np.round(edge['areal_density']/self.dataset.metadata['experiment']['flux_ppm']*1e-6, 2)
+            self.sidebar[10, 2].value = 'atoms/nm²'
+        
+    
+    def do_fit(self, value=0):
+        if 'experiment' in self.dataset.metadata:
+            exp = self.dataset.metadata['experiment']
+            if 'convergence_angle' not in exp:
+                raise ValueError('need a convergence_angle in experiment of metadata dictionary ')
+            alpha = exp['convergence_angle']
+            beta = exp['collection_angle']
+            beam_kv = exp['acceleration_voltage']
+
+        else:
+            raise ValueError('need a experiment parameter in metadata dictionary')
+        
+        eff_beta = eels.effective_collection_angle(self.energy_scale, alpha, beta, beam_kv)
+
+        self.low_loss = None
+        if self.sidebar[12, 1].value:
+            for key in self.datasets.keys():
+                if key != self.key:
+                    if isinstance(self.datasets[key], sidpy.Dataset):
+                        if self.datasets[key].data_type.name == 'SPECTRUM':
+                            if self.datasets[key].energy_loss[0] < 0:
+                                self.low_loss = self.datasets[key]/self.datasets[key].sum()
+
+        edges = eels.make_cross_sections(self.edges, np.array(self.energy_scale), beam_kv, eff_beta, self.low_loss)
+
+        if self.dataset.data_type == sidpy.DataType.SPECTRAL_IMAGE:
+            spectrum = self.view.get_spectrum()
+        else:
+            spectrum = self.dataset
+        self.edges = eels.fit_edges2(spectrum, self.energy_scale, edges)
+        areal_density = []
+        elements = []
+        for key in edges:
+            if key.isdigit():  # only edges have numbers in that dictionary
+                elements.append(edges[key]['element'])
+                areal_density.append(edges[key]['areal_density'])
+        areal_density = np.array(areal_density)
+        out_string = '\nRelative composition: \n'
+        for i, element in enumerate(elements):
+            out_string += f'{element}: {areal_density[i] / areal_density.sum() * 100:.1f}%  '
+
+        self.model = self.edges['model']['spectrum']
+        self.update()
+        self.plot()
+
+    def do_all_button_click(self, value=0):
+            if self.sidebar[13,0].value==False:
+                return
+            
+            if self.dataset.data_type.name != 'SPECTRAL_IMAGE':
+                self.do_fit()
+                return
+
+            if 'experiment' in self.dataset.metadata:
+                exp = self.dataset.metadata['experiment']
+                if 'convergence_angle' not in exp:
+                    raise ValueError('need a convergence_angle in experiment of metadata dictionary ')
+                alpha = exp['convergence_angle']
+                beta = exp['collection_angle']
+                beam_kv = exp['acceleration_voltage']
+            else:
+                raise ValueError('need a experiment parameter in metadata dictionary')
+
+            eff_beta = eels.effective_collection_angle(self.energy_scale, alpha, beta, beam_kv)
+            eff_beta = beta
+            self.low_loss = None
+            if self.sidebar[12, 1].value:
+                for key in self.datasets.keys():
+                    if key != self.key:
+                        if isinstance(self.datasets[key], sidpy.Dataset):
+                            if 'SPECTR' in self.datasets[key].data_type.name:
+                                if self.datasets[key].energy_loss[0] < 0:
+                                    self.low_loss = self.datasets[key]/self.datasets[key].sum()
+
+            edges = eels.make_cross_sections(self.edges, np.array(self.energy_scale), beam_kv, eff_beta, self.low_loss)
+    
+            view = self.view
+            bin_x = view.bin_x
+            bin_y = view.bin_y
+
+            start_x = view.x
+            start_y = view.y
+
+            number_of_edges = 0
+            for key in self.edges:
+                if key.isdigit():
+                    number_of_edges += 1
+
+            results = np.zeros([int(self.dataset.shape[0]/bin_x), int(self.dataset.shape[1]/bin_y), number_of_edges])
+            total_spec = int(self.dataset.shape[0]/bin_x)*int(self.dataset.shape[1]/bin_y)
+            self.sidebar[13,1].max = total_spec
+            #self.ui.progress.setMaximum(total_spec)
+            #self.ui.progress.setValue(0)
+            ind = 0
+            for x in range(int(self.dataset.shape[0]/bin_x)):
+                for y in range(int(self.dataset.shape[1]/bin_y)):
+                    ind += 1
+                    self.sidebar[13,1].value = ind
+                    view.x = x*bin_x
+                    view.y = y*bin_y
+                    spectrum = view.get_spectrum()
+                    with warnings.catch_warnings():
+                        warnings.simplefilter("ignore")
+                        edges = eels.fit_edges2(spectrum, self.energy_scale, edges)
+                    for key, edge in edges.items():
+                        if key.isdigit():
+                            # element.append(edge['element'])
+                            results[x, y, int(key)] = edge['areal_density']
+            edges['spectrum_image_quantification'] = results
+            self.sidebar[13,1].value = total_spec
+            view.x = start_x
+            view.y = start_y
+            self.sidebar[13,0].value = False
+            
+    
+    def modify_onset(self, value=-1):
+        edge_index = self.sidebar[4, 0].value
+        edge = self.edges[str(edge_index)]
+        edge['onset'] = self.sidebar[7,0].value
+        if 'original_onset' not in edge:
+            edge['original_onset'] = edge['onset']
+        edge['chemical_shift'] = edge['onset'] -  edge['original_onset']
+        self.update()
+        
+            
+    def modify_start_exclude(self, value=-1):
+        edge_index = self.sidebar[4, 0].value
+        edge = self.edges[str(edge_index)]
+        edge['start_exclude'] = self.sidebar[8,0].value
+        self.plot()
+        
+    def modify_end_exclude(self, value=-1):
+        edge_index = self.sidebar[4, 0].value
+        edge = self.edges[str(edge_index)]
+        edge['end_exclude'] = self.sidebar[9,0].value
+        self.plot()
+    
+    def modify_areal_density(self, value=-1):
+        edge_index = self.sidebar[4, 0].value
+        edge = self.edges[str(edge_index)]
+        
+        edge['areal_density'] = self.sidebar[10, 0].value
+        if self.y_scale != 1.0:
+            dispersion = self.energy_scale[1]-self.energy_scale[0]
+            edge['areal_density'] = self.sidebar[10, 0].value *self.dataset.metadata['experiment']['flux_ppm']/1e-6
+
+        self.model = self.edges['model']['background']
+        for key in self.edges:
+            if key.isdigit():
+                if 'data' in self.edges[key]:
+
+                    self.model = self.model + self.edges[key]['areal_density'] * self.edges[key]['data']
+        self.plot()
+
+    def set_action(self):
+        self.sidebar[1, 0].observe(self.set_fit_area, names='value')
+        self.sidebar[2, 0].observe(self.set_fit_area, names='value')
+        
+        self.sidebar[3, 0].on_click(self.find_elements)
+        self.sidebar[4, 0].observe(self.update, names='value')
+        self.sidebar[5, 0].observe(self.set_element, names='value')
+
+        self.sidebar[7, 0].observe(self.modify_onset, names='value')
+        self.sidebar[8, 0].observe(self.modify_start_exclude, names='value')
+        self.sidebar[9, 0].observe(self.modify_end_exclude, names='value')
+        self.sidebar[10, 0].observe(self.modify_areal_density, names='value')
+        
+        self.sidebar[11, 0].on_click(self.do_fit)
+        self.sidebar[12, 2].observe(self.plot, names='value')
+        self.sidebar[0, 0].observe(self.plot, names='value')
+        self.sidebar[12,0].observe(self.set_y_scale, names='value')
+        self.sidebar[13,0].observe(self.do_all_button_click, names='value')
+
+        self.elements_cancel_button.on_click(self.set_figure_pane)
+        self.elements_auto_button.on_click(self.auto_id)
+        self.elements_select_button.on_click(self.set_elements)